Entering edit mode
Dino Jolic
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10
@dino-jolic-5643
Last seen 10.6 years ago
Hi,
I had IRanges Version: 1.14.4 installed before and recently I had to
reinstall all of my R packages. Now, I've got an error while
installing the newer 1.16.4
* installing *source* package ?IRanges? ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
AEbufs.c -o AEbufs.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
CompressedList_class.c -o CompressedList_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
DataFrame_class.c -o DataFrame_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
GappedRanges_class.c -o GappedRanges_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
Grouping_class.c -o Grouping_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
Hits_class.c -o Hits_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
IRanges_constructor.c -o IRanges_constructor.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
IRanges_utils.c -o IRanges_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
IntervalTree.c -o IntervalTree.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
R_init_IRanges.c -o R_init_IRanges.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
RangedData_class.c -o RangedData_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
Ranges_comparison.c -o Ranges_comparison.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
RleViews_utils.c -o RleViews_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
Rle_class.c -o Rle_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
Rle_utils.c -o Rle_utils.o
Rle_utils.c: In function ?Rle_integer_runq?:
Rle_utils.c:735:6: warning: implicit declaration of function
?roundingScale? [-Wimplicit-function-declaration]
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
SEXP_utils.c -o SEXP_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
SharedDouble_utils.c -o SharedDouble_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
SharedInteger_utils.c -o SharedInteger_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
SharedRaw_utils.c -o SharedRaw_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
SharedVector_class.c -o SharedVector_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
SimpleList_class.c -o SimpleList_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
Vector_class.c -o Vector_class.o
Vector_class.c: In function ?vector_seqselect?:
Vector_class.c:95:4: warning: implicit declaration of function
?UNIMPLEMENTED_TYPE? [-Wimplicit-function-declaration]
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
XDoubleViews_utils.c -o XDoubleViews_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
XIntegerViews_utils.c -o XIntegerViews_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
XRawList_comparison.c -o XRawList_comparison.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
XVectorList_class.c -o XVectorList_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
XVector_class.c -o XVector_class.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
common.c -o common.o
common.c: In function ?firstWordInFile?:
common.c:1787:6: warning: ignoring return value of ?fgets?, declared
with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
compact_bitvector.c -o compact_bitvector.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
coverage.c -o coverage.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
dlist.c -o dlist.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
encode_overlaps.c -o encode_overlaps.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
errabort.c -o errabort.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
hash_utils.c -o hash_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
int_utils.c -o int_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
localmem.c -o localmem.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
memalloc.c -o memalloc.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
rbTree.c -o rbTree.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
safe_arithm.c -o safe_arithm.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
sort_utils.c -o sort_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
str_utils.c -o str_utils.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
ucsc_handlers.c -o ucsc_handlers.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c
vector_copy.c -o vector_copy.o
gcc -std=gnu99 -shared -o IRanges.so AEbufs.o
CompressedIRangesList_class.o CompressedList_class.o DataFrame_class.o
GappedRanges_class.o Grouping_class.o Hits_class.o IRanges_class.o
IRanges_constructor.o IRanges_utils.o IntervalTree.o
Ocopy_byteblocks.o R_init_IRanges.o RangedData_class.o
Ranges_comparison.o RleViews_utils.o Rle_class.o Rle_utils.o
SEXP_utils.o SharedDouble_utils.o SharedInteger_utils.o
SharedRaw_utils.o SharedVector_class.o SimpleList_class.o
SimpleRangesList_class.o Vector_class.o XDoubleViews_utils.o
XIntegerViews_utils.o XRawList_comparison.o XVectorList_class.o
XVector_class.o anyMissing.o common.o compact_bitvector.o coverage.o
dlist.o encode_overlaps.o errabort.o hash_utils.o int_utils.o
localmem.o memalloc.o rbTree.o safe_arithm.o sort_utils.o str_utils.o
ucsc_handlers.o vector_copy.o -L/usr/lib/R/lib -lR
installing to /ebio/abt6/djolic/Rdir/IRanges/libs
** R
** inst
** preparing package for lazy loading
Error : object ?mcmapply? is not exported by 'namespace:parallel'
ERROR: lazy loading failed for package ?IRanges?
I looked into the NAMESPACE file and there is a change from the
previous version, such as:
importFrom(parallel, mclapply, mcmapply)
Could this just be the cause?
Naively, I just tried removing the line and the install goes on, but
crashes at a latter point.
Thanks,
Dino
